Variant report

Variant	rs1854414
Chromosome Location	chr9:13129354-13129355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10116304	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10116749	0.84[EUR][1000 genomes]
rs10122431	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10125770	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10511577	0.85[EUR][1000 genomes]
rs10733254	0.87[EUR][1000 genomes]
rs10738323	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10738324	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10738325	0.87[EUR][1000 genomes]
rs10756454	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756455	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756456	0.89[EUR][1000 genomes]
rs10756457	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10756458	0.85[EUR][1000 genomes]
rs10756459	0.86[EUR][1000 genomes]
rs10809906	0.80[ASN][1000 genomes]
rs10809907	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10809908	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10809912	0.85[EUR][1000 genomes]
rs10960955	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10960958	0.85[EUR][1000 genomes]
rs10960959	0.85[EUR][1000 genomes]
rs1331668	0.93[EUR][1000 genomes]
rs1331670	0.82[EUR][1000 genomes]
rs1331672	0.86[EUR][1000 genomes]
rs1360058	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16930137	0.83[ASN][1000 genomes]
rs1854907	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1854908	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1854909	0.87[EUR][1000 genomes]
rs1929541	0.85[EUR][1000 genomes]
rs2225483	0.83[EUR][1000 genomes]
rs2297003	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35068818	0.91[EUR][1000 genomes]
rs3818595	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4237130	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6474753	0.84[EUR][1000 genomes]
rs6474754	0.84[EUR][1000 genomes]
rs6474755	0.87[EUR][1000 genomes]
rs7024892	0.96[EUR][1000 genomes]
rs7035244	0.92[EUR][1000 genomes]
rs7037704	0.87[EUR][1000 genomes]
rs7039646	0.96[EUR][1000 genomes]
rs7040347	0.85[EUR][1000 genomes]
rs7859465	0.84[EUR][1000 genomes]
rs7867993	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7871112	0.92[EUR][1000 genomes]
rs7871575	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9886797	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917331	chr9:12941193-13146852	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892582	chr9:13085379-13147764	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13097800-13139400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:13101600-13141600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:13103200-13134600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:13103200-13137200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:13103200-13143400	Weak transcription	Pancreas	Pancrea
6	chr9:13103200-13163400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:13103200-13175600	Weak transcription	HepG2	liver
8	chr9:13103400-13134600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:13103800-13139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:13104400-13137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:13105600-13134800	Weak transcription	Lung	lung
12	chr9:13105600-13144600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:13106000-13153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:13106600-13139200	Weak transcription	NHEK	skin
15	chr9:13109200-13138800	Weak transcription	Spleen	Spleen
16	chr9:13109200-13139400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:13111200-13134800	Weak transcription	Fetal Brain Male	brain
18	chr9:13112200-13143600	Weak transcription	Gastric	stomach
19	chr9:13112400-13134600	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:13113400-13134800	Weak transcription	Psoas Muscle	Psoas
21	chr9:13114200-13135000	Weak transcription	NHLF	lung
22	chr9:13114400-13132200	Weak transcription	Brain Substantia Nigra	brain
23	chr9:13114600-13139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:13114600-13139400	Weak transcription	NHDF-Ad	bronchial
25	chr9:13116000-13139800	Strong transcription	Liver	Liver
26	chr9:13118000-13139000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:13118200-13138800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:13118400-13139600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:13118800-13139600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:13118800-13139800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:13119000-13137200	Weak transcription	Esophagus	oesophagus
32	chr9:13119600-13134600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:13121600-13225200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr9:13121800-13139800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:13122200-13131800	Weak transcription	Brain Germinal Matrix	brain
36	chr9:13122400-13134800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:13122400-13134800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:13122400-13134800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:13122600-13186400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr9:13123200-13130400	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:13123200-13134800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:13123400-13130800	Weak transcription	Left Ventricle	heart
43	chr9:13123400-13131400	Weak transcription	Aorta	Aorta
44	chr9:13123400-13131400	Weak transcription	Fetal Stomach	stomach
45	chr9:13123400-13131600	Weak transcription	Placenta	Placenta
46	chr9:13123400-13136400	Weak transcription	Fetal Intestine Small	intestine
47	chr9:13124800-13135400	Weak transcription	Fetal Heart	heart
48	chr9:13125400-13130400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:13125400-13130400	Weak transcription	Ovary	ovary
50	chr9:13125400-13130400	Weak transcription	Stomach Smooth Muscle	stomach

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